Histone deacetylases (hereinafter also referred as HDACs) are known to play an essential role in the transcriptional machinery for regulating gene expression, induce histone hyperacetylation and to affect the gene expression. Therefore, it is a target of a therapeutic or prophylactic agent for diseases caused by abnormal gene expression such as inflammatory disorders, diabetes, diabetic complications, homozygous thalassemia, fibrosis, cirrhosis, acute promyelocytic leukemia (APL), organ transplant rejections, autoimmune diseases, protozoal infections, tumors, etc., to inhibit HDAC proteins.
Acetylation and deacetylation of histones are carried out by histone acetyl transferases (HAT) and histone deacetylases (HDACs). The state of acetylation of histones is an important determinant of gene transcription. Deacetylation is generally associated with reduced transcription of genes whereas increased acetylation of histones as induced by the action of HDAC inhibitors results in greater transcription of genes. Thus, HDAC inhibitors affect multiple processes in the cell which are likely to depend upon the dynamic state of the cell with respect to its capabilities of replication and differentiation.
The study of inhibitors of histone deacetylases indicates that these enzymes play an important role in cell proliferation and differentiation. The inhibitor Trichostatin A (TSA) (Yoshida et al. (1990) “Structural specificity for biological activity of trichostatin A, a specific inhibitor of mammalian cell cycling with potent differentiation-inducing activity in Friend leukemia cells” J. Antibiot. 43(9):1101-6), causes cell cycle arrest at both G1 and G2 phases (Yoshida and Beppu, (1988) “Reversible arrest of proliferation of rat 3Y1 fibroblasts in both the G1 and G2 phases by trichostatin A” Exp Cell Res. 177(1):122-31), reverts the transformed phenotype of different cell lines, and induces differentiation of Friend leukemia cells and others. TSA and suberoylanilide hydroxamic acid (SAHA) have been reported to inhibit cell growth, induce terminal differentiation, and prevent the formation of tumours in mice (Finnin et al., (1999) “Structures of a histone deacetylase homologue bound to the TSA and SAHA inhibitors” Nature 401, 188-193).
Cell cycle arrest by TSA correlates with an increased expression of gelsolin (Hoshikawa et al., (1994) “Trichostatin A induces morphological changes and gelsolin expression by inhibiting histone deacetylase in human carcinoma cell lines” Exp Cell Res. 214(1):189-97), an actin regulatory protein that is down regulated in malignant breast cancer (Mielnicki et al., (1999) “Epigenetic Regulation of Gelsolin Expression in Human Breast Cancer Cells” Experimental Cell Research, 249(1) pp. 161-176). Similar effects on cell cycle and differentiation have been observed with a number of deacetylase inhibitors (Kim et al., (1999) “Selective Induction of Cyclin-Dependent Kinase Inhibitors and Their Roles in Cell Cycle Arrest Caused by Trichostatin A, an Inhibitor of Histone Deacetylase” Ann. N.Y. Acad. Sci. 886: 200-203).
Trichostatin A has also been reported to be useful in the treatment of fibrosis, e.g., liver fibrosis and liver cirrhosis. See, e.g., Geerts et al., (1998) “Hepatic Stellate Cells and Liver Retinoid Content in Alcoholic Liver Disease in Humans” Clinical and Experimental Research 22 (2), 494-500.
Recently, certain compounds that induce differentiation have been reported to inhibit histone deacetylases. Several experimental antitumour compounds, such as trichostatin A (TSA), trapoxin, suberoylanilide hydroxamic acid (SAHA), and phenylbutyrate have been reported to act, at least in part, by inhibiting histone deacetylase (see, e.g., Yoshida et al. (1990) “Structural specificity for biological activity of trichostatin A, a specific inhibitor of mammalian cell cycle with potent differentiation-inducing activity in Friend leukemia cells” J. Antibiot. 43(9):1101-6; Richon et al., (1998) “A class of hybrid polar inducers of transformed cell differentiation inhibits histone deacetylases” PNAS 95(6) 3003-3007; and Kijima et al., (1993) “Trapoxin, an antitumor cyclic tetrapeptide, is an irreversible inhibitor of mammalian histone deacetylase” J. Biol. Chem., 268(30) 22429-22435). Additionally, diallyl sulfide and related molecules (see, e.g., Lea et al., (1999) “Increased acetylation of histones induced by diallyl disulfide and structurally related molecules” Int J Oncol. 15(2):347-52), oxamflatin (see, e.g., Kim et al., (1999) “Selective Induction of Cyclin-Dependent Kinase Inhibitors and Their Roles in Cell Cycle Arrest Caused by Trichostatin A, an Inhibitor of Histone Deacetylase” Ann. N.Y. Acad. Sci. 886: 200-203), MS-27-275, a synthetic benzamide derivative (see, e.g., Saito et al., (1999) “A synthetic inhibitor of histone deacetylase, MS-27-275, with marked in vivo antitumor activity against human tumors” PNAS 96(8) 4592-4597; Suzuki et al., (1999) “Synthesis and Histone Deacetylase Inhibitory Activity of New Benzamide Derivatives” J. Med. Chem., 42 (15), 3001-3003; note that MS-27 275 was later re-named as MS-275); butyrate derivatives (see, e.g., Lea and Tulsyan, (1995) “Discordant effects of butyrate analogues on erythroleukemia cell proliferation, differentiation and histone deacetylase” Anticancer Res. 15(3):879-83), FR901228 (see, e.g., Nokajima et al., 1998), depudecin (see, e.g., Kwon et al., (1998) “Depudecin induces morphological reversion of transformed fibroblasts via the inhibition of histone deacetylase” PNAS 95(7) 3356-3361), and m-carboxycinnamic acid bishydroxamide (see, e.g., Richon et al., 1998) have been reported to inhibit histone deacetylases. In vitro, some of these compounds are reported to inhibit the growth of fibroblast cells by causing cell cycle arrest in the G1 and G2 phases, and can lead to the terminal differentiation and loss of transforming potential of a variety of transformed cell lines (see, e.g., Richon et al, 1996; Kim et al., 1999; Yoshida et al., 1995; Yoshida & Beppu, 1988 (full cites provided earlier)). In vivo, phenylbutyrate is reported to be effective in the treatment of acute promyelocytic leukemia in conjunction with retinoic acid (see, e.g., Warrell et al., (1998) “Therapeutic Targeting of Transcription in Acute Promyelocytic Leukemia by Use of an Inhibitor of Histone Deacetylase” Journal of the National Cancer Institute, Vol. 90, No. 21, 1621-1625). SAHA is reported to be effective in preventing the formation of mammary tumours in rats, and lung tumors in mice (see, e.g., Desai et al., 1999).
The clear involvement of HDACs in the control of cell proliferation and differentiation suggest that aberrant HDAC activity may play a role in cancer. The most direct demonstration that deacetylases contribute to cancer development comes from the analysis of different acute promyelocytic leukaemias (APL). In most APL patients, a translocation of chromosomes 15 and 17 (t(15; 17)) results in the expression of a fusion protein containing the N-terminal portion of PML gene product linked to most of RARα (retinoic acid receptor). In some cases, a different translocation (t(11; 17)) causes the fusion between the zinc finger protein PLZF and RARα. In the absence of ligand, the wild type RARα represses target genes by tethering HDAC repressor complexes to the promoter DNA. During normal hematopoiesis, retinoic acid (RA) binds RARα and displaces the repressor complex, allowing expression of genes implicated in myeloid differentiation. The RARα fusion proteins occurring in APL patients are no longer responsive to physiological levels of RA and they interfere with the expression of the RA-inducible genes that promote myeloid differentiation. This results in a clonal expansion of promyelocytic cells and development of leukemia. In vitro experiments have shown that TSA is capable of restoring RA-responsiveness to the fusion RARα proteins and of allowing myeloid differentiation. These results establish a link between HDACs and oncogenesis and suggest that HDACs are potential targets for pharmaceutical intervention in APL patients. (See, for example, Kitamura et al., (2000) “Histone deacetylase inhibitor but not arsenic trioxide differentiates acute promyelocytic leukaemia cells with t(11;17) in combination with all-trans retinoic acid” Brit. J. Hemat. 108(4) 696-702; David et al., (1998) “Histone deacetylase associated with mSin3A mediates repression by the acute promyelocytic leukemia-associated PLZF protein” Oncogene (1998) 16, 2549-2556; Lin et al., (1998) “Role of the histone deacetylase complex in acute promyelocytic leukaemia” Nature 391(6669):811-4).
Furthermore, different lines of evidence suggest that HDACs may be important therapeutic targets in other types of cancer. Cell lines derived from many different cancers (prostate, colorectal, breast, neuronal, hepatic) are induced to differentiate by HDAC inhibitors (Yoshida and Horinouchi, (1999) “Trichostatin and Leptomycin: Inhibition of Histone Deacetylation and Signal-Dependent Nuclear Export” Annals of the New York Academy of Sciences 886:23-35). A number of HDAC inhibitors have been studied in animal models of cancer. They reduce tumor growth and prolong the lifespan of mice bearing different types of transplanted tumours, including melanoma, leukemia, colon, lung and gastric carcinomas, etc. (Ueda et al., (1994) “Serum levels of cytokines in patients with colorectal cancer: Possible involvement of interleukin-6 and interleukin-8 in hematogenous metastasis” 29(4); Kim et al., 1999).
Several of the known HDAC inhibitors have been found to be protective in different cellular and animal models of acute and chronic neurodegenerative injury and disease, for example, ischemic stroke, multiple sclerosis, and polyglutamine-expansion diseases, such as Huntington's disease and spinal and bulbar muscular atrophy (SBMA) (Kozikowski et al, J. Med. Chem. (2007), 50, 3054-3061). Furthermore, recent findings suggest that HDAC inhibitors can ameliorate deficits in synaptic plasticity, cognition, and stress-related behaviors in a wide range of neurologic and psychiatric disorders including Huntington's disease, Parkinson's disease, anxiety and mood disorders, Rubinstein-Taybi syndrome, and Rett syndrome (Abel, T. and Zukin, R. S., Current Opinion in Pharmacology (2008) 8:57-64). Beglopoulos and Shen (Beglopoulos, V. and Shen, J., TRENDS in Pharmacological Sciences (2006) 27:33-40) found that inhibitors of phosphodiesterase 4 and histone deacetylases reduce memory deficits and neurodegeneration in animal models of AD affecting cAMP response element (CRE) genes. Recently, Fischer et al (Fischer, A. et al., Nature (2007) 447:178-182) reported improved learning behavior and access to long-term memories after significant neuronal loss and brain atrophy can be reestablished in a mouse model by environmental enrichment and by treatment with inhibitors of histone deacetylases (see reviews and commentaries by Sweat, J. D. et al., Nature (2007) 447:151-152; Mangan, K. P. and Levenson, J. M., Cell (2007) 129:851-853; Albert, M. S., New Engl. J. Med. (2007) 357(5):502-503; and Abel, T. and Zukin, R. S., Current Opinion in Pharmacology (2008) 8:57-64). There appears to be a poorly understood component of neurodegenerative diseases related to excessive histone deacetylase activity, or at least a condition of reduced acetylation of certain histones that is corrected by increased acetylation resulting in improved learning and memory. In this respect, inhibition of certain histone deacetylases with the compounds described herein may potentially prove to be advantageous in the treatment of neurodegenerative diseases such as AD.
It has been estimated that neurodegenerative diseases presently affect 20 million individuals worldwide. The cost for medical care of patients with AD, for example, was $91 billion in 2005 and is predicted to increase to $160 billion by 2010 (Burke, R. E., Pharmacology and Therapeutics (2007) 114:262-277). Despite considerable research on the etiology and pharmacologic treatment of these diseases, no therapy is known to delay their progression (Schapira, A. H. V. and Olanow, C. W., JAMA (2004) 291:358-364; Burke, R. E., Pharmacology and Therapeutics (2007) 114:262-277). Alzheimer's disease (AD) and other neurodegenerative diseases are called tauopathies because they are characterized by the accumulation of aggregates of the tau protein in neurons. Tau proteins promote the assembly and stabilization of microtubular structures in neurons. Neurodegenerative diseases such as AD are frequently characterized by impaired learning and memory. The mechanism(s) responsible for these most troublesome symptoms is associated with death of neuronal cells. At a molecular level, the basis for changes in memory formation and consolidation has been linked to the activity of histone deacetylylases chromatin structures (Korzus, E. et al., Neuron (2004) 42:961-972; Levenson, J. M. et al., The Journal of Biological Chemistry (2004) 279:40545-40559).
Histone deacetylases also play a significant role in inflammatory diseases (Hildemann et al. Appl Microbiol Biotechnol (2007), 75(3), 487-497; Riester et al. Appl Microbiol Biotechnol (2007), 75(3), 499-514; Adcock, I M. Br J Pharmacol (2007), 150(7), 829-831; Huang L, J Cell Physiol (2006), 209(3), 611-616). Diverse cellular functions including the regulation of inflammatory gene expression, DNA repair and cell proliferation are regulated by changes in the acetylation status of histones and non-histone proteins. Recently, in vitro and in vivo data indicate that HDAC inhibitors may be anti-inflammatory due to their effects on cell death acting through acetylation of non-histone proteins. Although there are concerns over the long-term safety of these agents, they may prove useful particularly in situations where current anti-inflammatory therapies are suboptimal (Adcock, I M. Br J Pharmacol (2007), 150(7), 829-831).
Histone deacetylase inhibitors are also proposed as potential anti-HIV agents targeting Zn functional groups in retroviral zinc finger domains, based on the hypothesis and data advanced by Song et al. (2002) “Synthesis and Biological Properties of Amino Acid Amide Ligand-Based Pyridinioalkanoyl Thioesters as Anti-HIV agents” Bioorganic & Medicinal Chemistry 10, 1263-1273.
Histone deactylase inhibitors are also proposed as potential inhibitors of cardiac hypertrophy based on the data advanced by the following references: WO 2007021682, WO 2006129105, WO 2007014029, WO 2006023603, U.S. Patent Application Publication No. 2007-0004771, U.S. Patent Application Publication 2007-0135433, U.S. Patent Application Publication 2006-0235231, EP 1663310, U.S. Patent Application Publication 2007-0135365, EP 1694688, EP 1715870, EP 1691891, JP 2007511528, EP 1699436, and JP 2007514665.
The major structural group of HDAC inhibitors includes a hydroxamic acid component, presumed to be critical to the inhibitory activity of these molecules by their ability to bind zinc. Several other types of zinc binding groups as components of novel HDAC inhibitors are under evaluation. We have developed a novel series of HDAC inhibitors using a mercaptobenzaminoyl group as the zinc binder and believe that this moiety could be used in place of the hydroxamic acid and other zinc binding moieties on all other HDAC inhibitors to potential advantage. The synthesis of these HDAC inhibitors is described herein.
The compounds disclosed herein are also active inhibitors of proliferation of human cancer cells. These compounds inhibit the activity of histone deacetylase 3 and histone deacetylase 4 (HDAC3 and HDAC4, respectively), and also affect the stability of N-CoR in human brain cell lines (U-87) when cells are exposed to these compounds in culture.